First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

PeerJ

Volumn 2015, Issue 1, 2015, Pages

  Sekiguchi, Yuji ^a   Ohashi, Akiko ^a   Parks, Donovan ^b   Yamauchi, Toshihiro ^c   Tyson, Gene ^b   Hugenholtz, Philip ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c Kubota Corp   (Japan)

Author keywords

Anaerobic biotechnology; Candidate phylum; Filamentous bulking; KSB3 phylum; Metagenomics; Wastewater treatment

Indexed keywords

RNA 16S;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; CELL SIZING (PROCESS); EPIFLUORESCENCE MICROSCOPY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE IDENTIFICATION; GENE SEQUENCE; GENOME ANALYSIS; GRAM STAINING; MAXIMUM LIKELIHOOD METHOD; METAGENOMICS; MORPHOLOGY; NONHUMAN; PHYLOGENETIC TREE; PHYLUM; PROTEIN ASSEMBLY; WASTE WATER MANAGEMENT;

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

EID: 84926443411     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.740     Document Type: Article

References (66)

1. Ahring BK. 2003a. Biomethanation I, Advances in biochemical engineering/biotechnology. Berlin: Springer.
2. Ahring BK. 2003b. Perspectives for anaerobic digestion. In: Biomethanation I, Advances in biochemical engineering/biotechnology. Berlin: Springer, 1-30.
3. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. 2013. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology 31:533-538 DOI 10.1038/nbt.2579.
4. Angelidaki I, Karakashev D, Batstone DJ, Plugge CM, Stams AJM. 2011. Biomethanation and its potential. Methods in Enzymology 494:327-351 DOI 10.1016/B978-0-12-385112-3.00016-0.
5. Aoki-Kinoshita KF, Kanehisa M. 2007. Gene annotation and pathway mapping in KEGG. Methods in Molecular Biology 396:71-91.
6. Ben-Jacob E, Becker I, Shapira Y, Levine H. 2004. Bacterial linguistic communication and social intelligence. Trends in Microbiology 12:366-372 DOI 10.1016/j.tim.2004.06.006.
7. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. 2007. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209 DOI 10.1186/1471-2105-8-209.
8. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578-579 DOI 10.1093/bioinformatics/btq683.
9. Caporaso JG, Bittinger K, Bushman FD, Desantis TZ, Andersen GL, Knight R. 2010a. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266-267 DOI 10.1093/bioinformatics/btp636.
10. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, WaltersWA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010b. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7:335-336 DOI 10.1038/nmeth.f.303.
11. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4:Article 2120 DOI 10.1038/ncomms3120.
12. Darling AE, Jospin G, Lowe E, Matsen IV FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243 DOI 10.7717/peerj.243.
13. Doetsch RN. 1981. Determinative methods of light microscopy. In: Gerhardt P, ed. Manual of methods for general bacteriology. Washington, D.C.: American Society for Microbiology, 21-33.
14. Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME Journal 6:1186-1199 DOI 10.1038/ismej.2011.189.
15. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Computational Biology 7:e1002195 DOI 10.1371/journal.pcbi.1002195.
16. Felsenstein J. 1989. PHYLIP-Phylogeny inference package (version 3.2). Cladistics 5:164-166.
17. Galperin MY. 2004. Bacterial signal transduction network in a genomic perspective. Environmental Microbiology 6:552-567 DOI 10.1111/j.1462-2920.2004.00633.x.
18. Hulshoff Pol LW, de Castro Lopes SI, Lettinga G, Lens PNL. 2004. Anaerobic sludge granulation. Water Research 38:1376-1389 DOI 10.1016/j.watres.2003.12.002.
19. Huntley S, Hamann N, Wegener-Feldbrügge S, Treuner-Lange A, Kube M, Reinhardt R, Klages S, Müller R, Ronning CM, NiermanWC, Søgaard-Andersen L. 2011. Comparative genomic analysis of fruiting body formation in Myxococcales. Molecular Biology and Evolution 28:1083-1097 DOI 10.1093/molbev/msq292.
20. Imelfort M, Parks DH, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW. 2014. GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2:e603 DOI 10.7717/peerj.603.
21. Jarrell KF, McBride MJ. 2008. The surprisingly diverse ways that prokaryotes move. Nature Reviews Microbiology 6:466-476 DOI 10.1038/nrmicro1900.
22. Kirby JR. 2009. Chemotaxis-like regulatory systems: unique roles in diverse bacteria. Annual Reviews in Microbiology 63:45-59 DOI 10.1146/annurev.micro.091208.073221.
23. KleerebezemR, Macarie H. 2003. Treating industrial wastewater: anaerobic digestion comes of age. Chemical Engineering 110:56-64.
24. Konstantinidis KT, Tiedje JM. 2005. Towards a genome-based taxonomy for prokaryotes. Journal of Bacteriology 187:6258-6264 DOI 10.1128/JB.187.18.6258-6264.2005.
25. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Research 19:1639-1645 DOI 10.1101/gr.092759.109.
26. Letunic I, Bork P. 2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research 39:W475-W478 DOI 10.1093/nar/gkr201.
27. Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589-595 DOI 10.1093/bioinformatics/btp698.
28. Li J, Hu B, Zheng P, Qaisar M, Mei L. 2008. Filamentous granular sludge bulking in a laboratory scale UASB reactor. Bioresource Technology 99:3431-3438 DOI 10.1016/j.biortech.2007.08.005.
29. Liu Y, Xu H-L, Yang S-F, Tay J-H. 2003. Mechanisms and models for anaerobic granulation in upflow anaerobic sludge blanket reactor. Water Research 37:661-673 DOI 10.1016/S0043-1354(02)00351-2.
30. Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrateactive enzymes database (CAZy) in 2013. Nucleic Acids Research 42:D490-D495 DOI 10.1093/nar/gkt1178.
31. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer K-H. 2004. ARB: a software environment for sequence data. Nucleic Acids Research 32:1363-1371 DOI 10.1093/nar/gkh293.
32. Mai X, Adams MW. 1996. Purification and characterization of two reversible and ADP-dependent acetyl coenzyme. A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology 178:5897-5903.
33. Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH. 2013. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Research 41:D348-D352 DOI 10.1093/nar/gks1243.
34. Markowitz VM, Chen I-MA, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. 2014. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Research 42:D568-D573 DOI 10.1093/nar/gkt919.
35. Mauriello EMF, Mignot T, Yang Z, Zusman DR. 2010. Gliding motility revisited: how do the myxobacteria move without flagella? Microbiology and Molecular Biology Reviews 74:229-249 DOI 10.1128/MMBR.00043-09.
36. McDonald D, Price MN, Goodrich J, Nawrocki EP, Desantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME Journal 6:610-618 DOI 10.1038/ismej.2011.139.
37. Mignot T, Kirby JR. 2008. Genetic circuitry controlling motility behaviors of Myxococcus xanthus. BioEssays 30:733-743 DOI 10.1002/bies.20790.
38. Moller S, Croning M, Apweiler R. 2001. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17:646-653 DOI 10.1093/bioinformatics/17.7.646.
39. Narihiro T, Terada T, Kikuchi K, Iguchi A, Ikeda M, Yamauchi T, Shiraishi K, Kamagata Y, Nakamura K, Sekiguchi Y. 2009. Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes and Environments 24:88-96 DOI 10.1264/jsme2.ME08561.
40. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. PeerJ PrePrints 2:e554v1 DOI 10.7287/peerj.preprints.554v1.
41. Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 26:1641-1650 DOI 10.1093/molbev/msp077.
42. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Research 40:D290-D301 DOI 10.1093/nar/gkr1065.
43. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. 2005. InterProScan: protein domains identifier. Nucleic Acids Research 33:W116-W120 DOI 10.1093/nar/gki442.
44. Rivière D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S, Weissenbach J, Li T, Camacho P, Sghir A. 2009. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. The ISME Journal 3:700-714 DOI 10.1038/ismej.2009.2.
45. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069 DOI 10.1093/bioinformatics/btu153.
46. Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H. 1999. Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Applied and Environmental Microbiology 65:1280-1288.
47. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498-2504 DOI 10.1101/gr.1239303.
48. Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. 2013. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Research 23:111-120 DOI 10.1101/gr.142315.112.
49. Sieber JR, McInerney MJ, Gunsalus RP. 2012. Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annual Review of Microbiology 66:429-452 DOI 10.1146/annurev-micro-090110-102844.
50. Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L, Leshkowitz D, Galatenko V, Nikolaev V, Mugasimangalam RC, Bransburg-Zabary S, Gutnick DL, Lancet D, Ben-Jacob E. 2010. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. BMC Genomics 11:710 DOI 10.1186/1471-2164-11-710.
51. Skerker JM, Prasol MS, Perchuk BS, Biondi EG, Laub MT. 2005. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biology 3:e334 DOI 10.1371/journal.pbio.0030334.
52. Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P. 2014. An expanded genomic representation of the phylum cyanobacteria. Genome Biology and Evolution 6:1031-1045 DOI 10.1093/gbe/evu073.
53. Sorek R, Kunin V, Hugenholtz P. 2008. CRISPR a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology 6:181-186 DOI 10.1038/nrmicro1793.
54. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690 DOI 10.1093/bioinformatics/btl446.
55. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23:1282-1288 DOI 10.1093/bioinformatics/btm098.
56. Swofford DL. 2003. PAUP*: phylogenetic analysis using parsimony. version 4.0b10. Available at http://paup.csit.fsu.edu/index.html.
57. Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56:564-577 DOI 10.1080/10635150701472164.
58. Tanner MA, Everett CL, Coleman WJ, Yang MM. 2000. Complex microbial communities inhabiting sulfide-rich black mud from marine coastal environments. Biotechnology et alia 8:1-16.
59. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research 28:33-36 DOI 10.1093/nar/28.1.33.
60. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. 2005. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Applied and Environmental Microbiology 71:6319-6324 DOI 10.1128/AEM.71.10.6319-6324.2005.
61. Van Lier JB. 2008. High-rate anaerobic wastewater treatment: diversifying from end-of-the-pipe treatment to resource-oriented conversion techniques. Water Science and Technology 57:1137-1148 DOI 10.2166/wst.2008.040.
62. VanwonterghemI, Jensen PD, Ho DP, Batstone DJ, Tyson GW. 2014. Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Current Opinion in Biotechnology 27:55-64 DOI 10.1016/j.copbio.2013.11.004.
63. Yamada T, Kikuchi K, Yamauchi T, Shiraishi K, Ito T, Okabe S, Hiraishi A, Ohashi A, Harada H, Kamagata Y, Nakamura K, Sekiguchi Y. 2011. Ecophysiology of uncultured filamentous anaerobes belonging to the phylum KSB3 that cause bulking in methanogenic granular sludge. Applied and Environmental Microbiology 77:2081-2087 DOI 10.1128/AEM.02475-10.
64. Yamada T, Sekiguchi Y. 2009. Cultivation of uncultured Chloroflexi subphyla: significance and ecophysiology of formerly uncultured Chloroflexi "subphylum I" with natural and biotechnological relevance. Microbes and Environments 24:205-216 DOI 10.1264/jsme2.ME09151S.
65. Yamada T, Yamauchi T, Shiraishi K, Hugenholtz P, Ohashi A, Harada H, Kamagata Y, Nakamura K, Sekiguchi Y. 2007. Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. The ISME Journal 1:246-255 DOI 10.1038/ismej.2007.28.
66. Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. 2012. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Research 40:W445-W451 DOI 10.1093/nar/gks479.